Patches are made in the same structure as the Zen Cart files ...

If you have the Patch files on the Left and your Site on the Right in your FTP program and can see:
/includes
ipn_main_handler.php

then both sides are correct and you can just overwrite the files on the Right (your site) with the files on the Left (your patch) ...

NOTE: don't forget that you should update your copy on your computer as well to have the new files ...